knitr document van Steensel lab
TF reporter barcode processing - Deep P53/GR scan - stimulation 2
Introduction
12,000 TF reporters on pMT06 were transfected into A549 & MCF7 cells, sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.
Analysis
Data exploration
-> Based on these figures I will exclude all samples that have less than 300 barcodes with at least 500 normalized counts.
Normalization of barcode counts:
Divide cDNA barcode counts through pDNA barcode counts, if more than 30 pDNA counts for that barcode
Calculate correlations between technical replicates
Data quality plots - correlation between replicates
Session Info
## [1] "Run time: 2.717482 mins"
## [1] "/DATA/usr/m.trauernicht/projects/SuRE_deep_scan_trp53_gr/stimulation_2_gcf6301"
## [1] "Tue Jan 12 11:10:28 2021"
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
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## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
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## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel stats graphics grDevices utils datasets
## [8] methods base
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## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 ggpointdensity_0.1.0
## [4] ggbiplot_0.55 scales_1.1.0 factoextra_1.0.7
## [7] shiny_1.4.0 pheatmap_1.0.12 gridExtra_2.3
## [10] RColorBrewer_1.1-2 readr_1.3.1 haven_2.2.0
## [13] ggbeeswarm_0.6.0 plotly_4.9.2.1 tibble_3.0.1
## [16] dplyr_0.8.5 vwr_0.3.0 latticeExtra_0.6-29
## [19] lattice_0.20-38 stringdist_0.9.5.5 GGally_1.5.0
## [22] ggpubr_0.2.5 magrittr_1.5 ggplot2_3.3.0
## [25] stringr_1.4.0 plyr_1.8.6 data.table_1.12.8
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.1 tidyr_1.0.0 splines_3.6.3 jsonlite_1.7.1
## [5] prettydoc_0.4.0 assertthat_0.2.1 vipor_0.4.5 yaml_2.2.1
## [9] ggrepel_0.8.1 pillar_1.4.3 glue_1.4.2 digest_0.6.27
## [13] promises_1.1.1 ggsignif_0.6.0 colorspace_1.4-1 Matrix_1.2-18
## [17] htmltools_0.5.0 httpuv_1.5.4 pkgconfig_2.0.3 purrr_0.3.3
## [21] xtable_1.8-4 jpeg_0.1-8.1 later_1.1.0.1 mgcv_1.8-31
## [25] farver_2.0.1 ellipsis_0.3.0 withr_2.1.2 lazyeval_0.2.2
## [29] crayon_1.3.4 mime_0.9 evaluate_0.14 nlme_3.1-143
## [33] forcats_0.4.0 beeswarm_0.2.3 tools_3.6.3 hms_0.5.3
## [37] lifecycle_0.2.0 munsell_0.5.0 compiler_3.6.3 rlang_0.4.8
## [41] htmlwidgets_1.5.2 crosstalk_1.0.0 labeling_0.3 rmarkdown_2.5
## [45] gtable_0.3.0 reshape_0.8.8 reshape2_1.4.4 R6_2.5.0
## [49] knitr_1.30 fastmap_1.0.1 stringi_1.5.3 Rcpp_1.0.5
## [53] vctrs_0.2.4 png_0.1-7 tidyselect_1.1.0 xfun_0.19